Flow chart of AMARE.

<p>Flow chart of AMARE.</p

Data set of Bonin et al. [11].

<p>The unrooted neighbor-joining trees are based on Nei-Li genetic distances calculated from A) the orignal character matrix with 328 markers (10 primer combinations), B) the original character matrix with 222 markers (the 5 primer combinations including replicates) and C) the AMARE masked character matrix with 158 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with • and are only shown for more basal splits. Each sample site is indicated by its own colour. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates Nei-Li distance.</p

Overview of character matrices and quality estimates.

<p>Selected character matrices are indicated in <b>bold</b>, original character matrices in <i>italics</i>.</p>*<p> = Nei-Li distances were used for resolution score, principal coordinate and stemminess analyses.</p><p>♦ = Uncorrected distances were used for resolution score, principal coordinate and stemminess analyses.</p><p>▪ = percentage of variation explained by the first three axes of the principle coordinate analyses (PCoA).</p

AMARE replicate transformation.

<p>This example shows how AMARE transforms replicates into pairs (<i>i,j</i>) representing the observed state 0 (fragment absence) or 1 (fragment presence) within each bin.</p

<i>Ipomoea</i> data set of Holland et al. [31].

<p>The neighbor-joining trees are based on uncorrected genetic distances calculated from A) the original character matrix with 1425 markers and B) the AMARE masked character matrix with 406 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with •. Replicated individuals are indicated in green. <i>Ipomoea tiliacea</i> represents the root of the tree. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates uncorrected genetic distance.</p

<i>Ourisia</i> data set of Holland et al.[31].

<p>The neighbor-joining trees are based on uncorrected genetic distances calculated from A) the original character matrix with 2011 markers and B) the AMARE masked character matrix with 530 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with • and are only shown for more basal splits. Replicated individuals are indicated in green. The Australian species <i>Ourisia integrifolia</i> is sister to all New Zealand species and thus the root of the tree. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates uncorrected genetic distance.</p

Rooted neighbor-joining tree of the AMARE reduced character matrix of Dasmahapatra et al. [8].

<p>The AMARE reduced character matrix comprised 108 selected markers. The tree is based on Nei-Li genetic distances. Numbers represent % bootstrap support obtained from 1000 bootstrap replicates and are shown only when ≥50%. Replicated individuals are indicated in green. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates Nei-Li distance.</p

Sampling localities of specimens of <i>Theba</i> on Lanzarote and Fuerteventua.

<p>The Jandía peninsula is enlarged for better recognition. * = ∼20 specimens collected, ▪ = fewer than 20 specimens collected, ○ = empty shells.</p

Isolation by distance (IBD).

<p>A) Pairwise F_ST values for all populations based on AFLP data versus geographical distances between all sample sites in kilometers. B) Pairwise F_ST values for all populations of <i>Theba</i> sp. 1a, <i>Theba</i> sp. 1b, <i>Theba</i> sp. 4 and <i>T.</i> cf.<i>clausoinflata</i> “Rock” based on AFLP data versus geographical distances between corresponding sample sites in kilometers.</p

Principal component scatterplot (component 1 versus 2).

<p>The analysis was based on geometric morphometrics of ten shell parameters. Convex hulls circumscribe the areas occupied by each MOTU.</p